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New Single Cell Tutorial in R #4141

Merged
merged 86 commits into from
Oct 2, 2023
Merged

New Single Cell Tutorial in R #4141

merged 86 commits into from
Oct 2, 2023

Commits on May 17, 2023

  1. Edited text

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  2. Edited text

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  3. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

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    Camila-goclowski authored May 17, 2023
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  4. Preamble edited

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  5. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
    Camila-goclowski authored May 17, 2023
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  6. Reformatted tutorial.md

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  7. added cluster labelling might change filtering

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  8. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
    Camila-goclowski authored May 17, 2023
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Commits on Jun 13, 2023

  1. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
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  2. remainder of tutorial added

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  3. reformatting

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  4. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
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  5. Merge branch 'Filter,-Plot,-and-Explore_WIP' of https://github.com/Ca… 

    …mila-goclowski/training-material into Filter,-Plot,-and-Explore_WIP
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  6. removed tutorial.html per helena's rec

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  7. Helena's comments fixed--pt2

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  8. pt3

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Commits on Jun 29, 2023

  1. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
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  2. formatting changes

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Commits on Jul 10, 2023

  1. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
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  2. Merge branch 'Filter,-Plot,-and-Explore_WIP' of https://github.com/Ca… 

    …mila-goclowski/training-material into Filter,-Plot,-and-Explore_WIP
    @Camila-goclowski
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  3. code formatting fix

    @Camila-goclowski
    Camila-goclowski committed Jul 10, 2023
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  4. code formatting (equals) correction

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    Camila-goclowski committed Jul 10, 2023
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  5. code block formatting

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    Camila-goclowski committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. authorship correction

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  2. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
    Camila-goclowski authored Jul 11, 2023
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  3. recorrected contributors

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  4. jekyll fix--hopefully

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  5. fixed broken box?

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    Camila-goclowski committed Jul 11, 2023
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  6. jekyll fix in preamble

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  7. added first eight plots

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    Camila-goclowski committed Jul 11, 2023
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Commits on Jul 12, 2023

  1. code format test

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  2. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
    Camila-goclowski authored Jul 12, 2023
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  3. fixed blocking issue at 141

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    Camila-goclowski committed Jul 12, 2023
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  4. another block fix

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    Camila-goclowski committed Jul 12, 2023
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Commits on Jul 13, 2023

  1. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
    Camila-goclowski authored Jul 13, 2023
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  2. removed redundant library calling

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  3. made adding metadata a little less clunky

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    Camila-goclowski committed Jul 13, 2023
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  4. actually fixed block issue (extra space on 188)

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  5. added plots 9-12

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  6. added plots 13-17

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Commits on Aug 1, 2023

  1. formatting first half

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  2. finished first half formatting

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  3. second half formatting

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  4. almost done formatting -- missing 2 plots

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  5. added zonodo link

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  6. corrected and added final plots

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  7. line edits

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Commits on Aug 14, 2023

  1. line edits from Marisa

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Commits on Aug 16, 2023

  1. added where data comes from

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  2. added link to own history w/ data

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  3. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
    Camila-goclowski authored Aug 16, 2023
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  4. reformatted some tip/comment boxes

    @Camila-goclowski
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  5. Merge branch 'Filter,-Plot,-and-Explore_WIP' of https://github.com/Ca… 

    …mila-goclowski/training-material into Filter,-Plot,-and-Explore
    @Camila-goclowski
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  6. DE box fix

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  7. function fixes

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  8. broken boxes ID'd by lint check

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  9. two more potentisl broken boxes

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  10. corrected broken links

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    Camila-goclowski committed Aug 16, 2023
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  11. reword

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Commits on Aug 23, 2023

  1. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/preamble.md

Co-authored-by: Pavankumar Videm <[email protected]>
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  2. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/preamble.md

Co-authored-by: Pavankumar Videm <[email protected]>
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  3. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/preamble.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
    Camila-goclowski and pavanvidem authored Aug 23, 2023
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  4. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/tutorial.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
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Commits on Aug 30, 2023

  1. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/tutorial.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
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  2. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/tutorial.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
    Camila-goclowski and pavanvidem authored Aug 30, 2023
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  3. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/tutorial.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
    Camila-goclowski and pavanvidem authored Aug 30, 2023
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  4. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/tutorial.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
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  5. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/tutorial.md

Co-authored-by: Pavankumar Videm <[email protected]>
    @Camila-goclowski @pavanvidem
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  6. added zenodo and fixed hempty history

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  7. added zenodo link and fixed empty history link

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  8. Merge branch 'Filter,-Plot,-and-Explore_WIP' of https://github.com/Ca… 

    …mila-goclowski/training-material into Filter,-Plot,-and-Explore
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Commits on Sep 15, 2023

  1. reorganized Get Data section

    @Camila-goclowski
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  2. reformatted first hands on box in preamble

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  3. added plot 8 (genes x mito zoomed in)

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  4. added saving object and plots to end

    @Camila-goclowski
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  5. linting error link removed

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Commits on Sep 21, 2023

  1. Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

    @Camila-goclowski
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Commits on Sep 26, 2023

  1. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/preamble.md

Co-authored-by: Saskia Hiltemann <[email protected]>
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  2. added references for citations (tutorial.bib file)

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Commits on Sep 27, 2023

  1. replaced author list commas with "and"s in bib

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Commits on Oct 2, 2023

  1. Update topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRS… 

    …tudio-WIP/preamble.md
    @shiltemann
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  2. fix citations

    @shiltemann
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  3. Merge branch 'Filter,-Plot,-and-Explore_WIP' of github.com:Camila-goc… 

    …lowski/training-material into Filter,-Plot,-and-Explore_WIP
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  4. rename folder

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  5. move folder

    @shiltemann
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  6. Update dependencies to try and fix htmlproofer

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